The filter on the tophat2 fusions output wasn't being evaluated correctly when settingsType is preSet since the param dict wouldn't then have an entry for 'fusion_search'
$ hg diff tools/ngs_rna/tophat2_wrapper.xml diff -r 3f12146d6d81 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 14:10:56 2012 -0400 +++ b/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 15:47:47 2012 -0500 @@ -297,7 +297,7 @@
<outputs> <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"> - <filter>(params['fusion_search']['do_search'] == 'Yes')</filter> + <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter> </data> <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> <actions>